bims-instec 2023-09-24 papers

Gastroenterology. 2023 Sep 14. pii: S0016-5085(23)05002-3. [Epub ahead of print]

CXADR-Like Membrane Protein regulates colonic epithelial cell proliferation and prevents tumor growth.

Anny-Claude Luissint, Shuling Fan, Hikaru Nishio, Antonio M Lerario, Jael Miranda, Roland S Hilgarth, Jonas Cook, Asma Nusrat, Charles A Parkos.

BACKGROUND & AIMS: CXADR-Like Membrane Protein (CLMP) is structurally related to Coxsackie and Adenovirus Receptor. Pathogenic variants in CLMP gene have been associated with congenital short bowel syndrome, implying a role for CLMP in intestinal development. However, the contribution of CLMP to regulating gut development and homeostasis is unknown.
METHODS: In this study, we investigated CLMP function in the colonic epithelium using complementary in vivo and in vitro approaches including mice with inducible intestinal epithelial cell (IEC)-specific deletion of CLMP (ClmpΔIEC), intestinal organoids, IECs with overexpression or loss of CLMP and RNA-seq data from individuals with colorectal cancer (CRC).
RESULTS: Loss of CLMP enhanced IEC proliferation and conversely, CLMP overexpression reduced proliferation. Xenograft experiments revealed increased tumor growth in mice implanted with CLMP-deficient colonic tumor cells, while poor engraftment was observed with CLMP-overexpressing cells. ClmpΔIEC mice showed exacerbated tumor burden in an Azoxymethane/Dextran Sulfate Sodium-induced colonic tumorigenesis model, and CLMP expression was reduced in human CRC samples. Mechanistic studies revealed that CLMP-dependent regulation of IEC proliferation is linked to signaling through mTOR/Akt/β-catenin pathways.
CONCLUSIONS: These results reveal novel insights into CLMP function in the colonic epithelium, highlighting an important role in regulating IEC proliferation, suggesting tumor suppressive function in colon cancer.

Keywords: CAR-Like Membrane protein; Cell proliferation; Colorectal cancer; mTOR/Akt/β-catenin pathway

DOI: https://doi.org/10.1053/j.gastro.2023.09.012

bioRxiv. 2023 Sep 05. pii: 2023.09.04.556156. [Epub ahead of print]

KAT2 paralogs prevent dsRNA accumulation and interferon signaling to maintain intestinal stem cells.

Mai-Uyen Nguyen, Sarah Potgieter, Winston Huang, Julie Pfeffer, Sean Woo, Caifeng Zhao, Matthew Lawlor, Richard Yang, Angela Halstead, Sharon Dent, José B Sáenz, Haiyan Zheng, Zuo-Fei Yuan, Simone Sidoli, Christopher E Ellison, Michael Verzi.

Histone acetyltransferases KAT2A and KAT2B are paralogs highly expressed in the intestinal epithelium, but their functions are not well understood. In this study, double knockout of murine Kat2 genes in the intestinal epithelium was lethal, resulting in robust activation of interferon signaling and interferon-associated phenotypes including the loss of intestinal stem cells. Use of pharmacological agents and sterile organoid cultures indicated a cell-intrinsic double-stranded RNA trigger for interferon signaling. Acetyl-proteomics and dsRIP-seq were employed to interrogate the mechanism behind this response, which identified mitochondria-encoded double-stranded RNA as the source of intrinsic interferon signaling. Kat2a and Kat2b therefore play an essential role in regulating mitochondrial functions as well as maintaining intestinal health.
Highlights of the work: Kat2a and Kat2b double knockout in the murine intestinal epithelium triggers activation of the interferon signaling pathway Kat2a/Kat2b knockout leads to intestinal stem cell loss and other mucosal phenotypes consistent with interferon activation Histone PTM mass spec profiling reveals the first in vivo study showing H3K9ac-specific loss with Kat2a and Kat2b double knockout, yet without correlation to interferon signaling pathway genes Comprehensive proteomic analysis identifies non-histone acetyl-lysine targets of KAT2 in the mouse intestine in vivo, including mitochondrial proteins Mitochondrial function is compromised upon Kat2 loss dsRIP-seq identifies double-stranded RNA from the mitochondria as a trigger for the intrinsic immune response upon Kat2 double knockout.

DOI: https://doi.org/10.1101/2023.09.04.556156

J Gastrointest Oncol. 2023 Aug 31. 14(4): 1735-1745

SOX9 knockout decreases stemness properties in colorectal cancer cells.

Mariana Avendaño-Felix, Maribel Aguilar-Medina, José Geovanni Romero-Quintana, Alfredo Ayala-Ham, Adriana S Beltran, José F Olivares-Quintero, César López-Camarillo, Carlos Pérez-Plasencia, Mercedes Bermúdez, Erik Lizárraga-Verdugo, Jorge López-Gutierrez, Guzman Sanchez-Schmitz, Rosalío Ramos-Payán.

Background: Colorectal cancer (CRC) is a leading cause of death worldwide. SRY-box transcription factor 9 (SOX9) participates in organogenesis and cell differentiation in normal tissues but has been involved in carcinogenesis development. Cancer stem cells (CSCs) are a small population of cells present in solid tumors that contribute to increased tumor heterogeneity, metastasis, chemoresistance, and relapse. CSCs have properties such as self-renewal and differentiation, which can be modulated by many factors. Currently, the role of SOX9 in the maintenance of the stem phenotype has not been well elucidated, thus, in this work we evaluated the effect of the absence of SOX9 in the stem phenotype of CRC cells.
Methods: We knockout (KO) SOX9 in the undifferentiated CRC cell line HCT116 and evaluated their stemness properties using sphere formation assay, differentiation assay, and immunophenotyping.
Results: SOX9-KO affected the epithelial morphology of HCT116 cells and stemness characteristics such as its pluripotency signature with the increase of SOX2 as a compensatory mechanism to induce SOX9 expression, the increase of KLF4 as a differentiation feature, as well as the inhibition of the stem cell markers CD44 and CD73. In addition, SOX9-KO cells gain the epithelial-mesenchymal transition (EMT) phenotype with a significant upregulation of CDH2. Furthermore, our results showed a remarkable effect on first- and second-sphere formation, being SOX9-KO cells less capable of forming high-size-resistant spheres. Nevertheless, CSCs surface markers were not affected during the differentiation assay.
Conclusions: Collectively, our findings supply evidence that SOX9 promotes the maintenance of stemness properties in CRC-CSCs.

Keywords: CRISPR-Cas9; Colorectal cancer (CRC); SRY-box transcription factor 9 (SOX9); cancer stem cells; cancer stem cells (CSCs); stemness

DOI: https://doi.org/10.21037/jgo-22-1163

Commun Biol. 2023 Sep 21. 6(1): 962

BRAFV600E-mutated serrated colorectal neoplasia drives transcriptional activation of cholesterol metabolism.

BRAF mutations occur early in serrated colorectal cancers, but their long-term influence on tissue homeostasis is poorly characterized. We investigated the impact of short-term (3 days) and long-term (6 months) expression of BrafV600E in the intestinal tissue of an inducible mouse model. We show that BrafV600E perturbs the homeostasis of intestinal epithelial cells, with impaired differentiation of enterocytes emerging after prolonged expression of the oncogene. Moreover, BrafV600E leads to a persistent transcriptional reprogramming with enrichment of numerous gene signatures indicative of proliferation and tumorigenesis, and signatures suggestive of metabolic rewiring. We focused on the top-ranking cholesterol biosynthesis signature and confirmed its increased expression in human serrated lesions. Functionally, the cholesterol lowering drug atorvastatin prevents the establishment of intestinal crypt hyperplasia in BrafV600E-mutant mice. Overall, our work unveils the long-term impact of BrafV600E expression in intestinal tissue and suggests that colorectal cancers with mutations in BRAF might be prevented by statins.

DOI: https://doi.org/10.1038/s42003-023-05331-x

Metabolomics. 2023 Sep 20. 19(10): 84

Staging of colorectal cancer using lipid biomarkers and machine learning.

Sanduru Thamarai Krishnan, David Winkler, Darren Creek, Dovile Anderson, Chandra Kirana, Guy J Maddern, Kevin Fenix, Ehud Hauben, David Rudd, Nicolas Hans Voelcker.

INTRODUCTION: Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Alteration in lipid metabolism and chemokine expression are considered hallmark characteristics of malignant progression and metastasis of CRC. Validated diagnostic and prognostic biomarkers are urgently needed to define molecular heterogeneous CRC clinical stages and subtypes, as liver dominant metastasis has poor survival outcomes.
OBJECTIVES: The aim of this study was to integrate lipid changes, concentrations of chemokines, such as platelet factor 4 and interleukin 8, and gene marker status measured in plasma samples, with clinical features from patients at different CRC stages or who had progressed to stage-IV colorectal liver metastasis (CLM).
METHODS: High-resolution liquid chromatography-mass spectrometry (HR-LC-MS) was used to determine the levels of candidate lipid biomarkers in each CRC patient's preoperative plasma samples and combined with chemokine, gene and clinical data. Machine learning models were then trained using known clinical outcomes to select biomarker combinations that best classify CRC stage and group.
RESULTS: Bayesian neural net and multilinear regression-machine learning identified candidate biomarkers that classify CRC (stages I-III), CLM patients and control subjects (cancer-free or patients with polyps/diverticulitis), showing that integrating specific lipid signatures and chemokines (platelet factor-4 and interluken-8; IL-8) can improve prognostic accuracy. Gene marker status could contribute to disease prediction, but requires ubiquitous testing in clinical cohorts.
CONCLUSION: Our findings demonstrate that correlating multiple disease related features with lipid changes could improve CRC prognosis. The identified signatures could be used as reference biomarkers to predict CRC prognosis and classify stages, and monitor therapeutic intervention.

Keywords: Biomarker; Cancer Subtypes; Lipidomics; Machine learning; Metastatic colorectal cancer classification; Multi-omics

DOI: https://doi.org/10.1007/s11306-023-02049-z